Fig. 3: Changes in gene expression during neuronal differentiation.

A Changes in gene expression associated with the differentiation process in wildtype LUHMES cells. Genes with statistically significant changes in expression between consecutive time points of differentiation as assessed by EdgeR (FDR; quasi-likelihood F-test followed by Benjamini-Hochberg correction for multitesting) are marked red. Source data are provided in Supplementary Data 3. B Clusters representing various gene expression patterns associated with the differentiation of LUHMES cells, obtained by k-means clustering of RNA-seq data. k-means of 6 resulted in a good representation of expression patterns and separation of genes into clusters, as seen in the PCA analysis plot on the right. Each point on the plot represents a gene, genes are colored by clusters. C Heatmap representation of expression patterns of all the genes during differentiation of WT cells, separated by clusters. D Representation of GO terms associated with defined gene clusters, as analyzed by g::Profiler using default statistical parameters: Fishers’ one-tailed test and multiple testing correction algorithm g:SCS. Detailed outcome of the analysis is in Supplementary Data 2. Source data for the figure are provided as a Source Data file.